Rotifers are an important part of freshwater ecosystems. The Brachionus plicatilis species complex inhabits a wide range of freshwater habitats worldwide. This complex of at least 15 species is morphologically diverse, both within and between species, and likely inhabits many different niches within these ecosystems. As well as this range of morphologies, B. plicatilis spp. exhibits genome size variations up to 8-fold. This dramatic change in genome size across the species complex is likely the largest observed in such closely related animals. The consequences of such variation, on both the structure and composition of genome, and the biology of the species complex is unknown. One species in this complex, Brachionus asplanchnoidis, has genome sizes ranging from 205Mbp to 271Mbp. Genome sequencing and analysis of different populations from this species are the first step in understanding such large genome size changes on short evolutionary time-scales. These data can then be related to biological and ecological outcomes. Often, in similar cases of genome size variation in plants, these changes are largely driven by non-coding DNA. Initial analyses of B. asplanchnoidis genomes indicate that repetitive DNA sequences are partly responsible for a large part of the observed genome size variation. The identity and distribution of these repetitive sequences shed light on the influence of such sequences not only on genome size evolution, but also on rotifer biology.